1U2W

Crystal Structure of the Staphylococcus aureus pI258 CadC

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the Staphylococcus aureus pI258 CadC Cd(II)/Pb(II)/Zn(II)-responsive repressor

Ye, J., Kandegedara, A., Martin, P., Rosen, B.P.

(2005) J Bacteriol 187: 4214-4221

  • DOI: 10.1128/JB.187.12.4214-4221.2005
  • Primary Citation of Related Structures:  
    1U2W

  • PubMed Abstract: 

    • The Staphylococcus aureus plasmid pI258 cadCA operon encodes a P-type ATPase, CadA, that confers resistance to the heavy metals Cd(II), Zn(II), and Pb(II). Expression of this heavy-metal efflux pump is regulated by CadC, a homodimeric repressor that dissociates from the cad operator/promoter upon binding of Cd(II), Pb(II), or Zn(II) ...

    The Staphylococcus aureus plasmid pI258 cadCA operon encodes a P-type ATPase, CadA, that confers resistance to the heavy metals Cd(II), Zn(II), and Pb(II). Expression of this heavy-metal efflux pump is regulated by CadC, a homodimeric repressor that dissociates from the cad operator/promoter upon binding of Cd(II), Pb(II), or Zn(II). CadC is a member of the ArsR/SmtB family of metalloregulatory proteins. Here we report the X-ray crystal structure of CadC at 1.9 angstroms resolution. The dimensions of the protein dimer are approximately 30 angstroms by 40 angstroms by 70 angstroms. Each monomer contains six alpha-helices and a three-stranded beta-sheet. Helices 4 and 5 form a classic helix-turn-helix motif that is the putative DNA binding region. The alpha1 helix of one monomer crosses the dimer to approach the alpha4 helix of the other monomer, consistent with the previous proposal that these two regulatory metal binding sites for the inducer cadmium or lead are each formed by Cys-7 and Cys-11 from the N terminus of one monomer and Cys-58 and Cys-60 of the other monomer. Two nonregulatory metal binding sites containing zinc are formed between the two antiparallel alpha6 helices at the dimerization interface. This is the first reported three-dimensional structure of a member of the ArsR/SmtB family with regulatory metal binding sites at the DNA binding domain and the first structure of a transcription repressor that responds to the heavy metals Cd(II) and Pb(II).

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, 540 E. Canfield Ave., Detroit, MI 48201, USA. .



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cadmium efflux system accessory proteinA, B, C, D122Staphylococcus aureusMutation(s): 1 
Gene Names: cadC
UniProt
Find proteins for P20047 (Staphylococcus aureus)
Explore P20047 
Go to UniProtKB:  P20047
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20047
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.536α = 90
b = 116.536β = 90
c = 41.842γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations